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Crystal structure of the human 2-oxoglutarate oxygenase LOC390245
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OQ7 PDB ENTRY 2OQ7
Crystallization Crystal Properties Matthews coefficient Solvent content 2.29 46.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.904 α = 90 b = 111.009 β = 90 c = 224.199 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2008-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 99 99.9 0.06 10.1 4.2 63031 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.23 99.4 0.49 1.8 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2OQ7 2.1 111.8 63031 3333 99.9 0.212 0.21 0.234 0.236 0.2492 RANDOM 14.83
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.29 -0.42 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.538 r_dihedral_angle_3_deg 13.969 r_dihedral_angle_4_deg 13.065 r_dihedral_angle_1_deg 10.036 r_scangle_it 6.281 r_scbond_it 4.344 r_mcangle_it 2.781 r_mcbond_it 1.582 r_angle_refined_deg 1.326 r_angle_other_deg 0.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.538 r_dihedral_angle_3_deg 13.969 r_dihedral_angle_4_deg 13.065 r_dihedral_angle_1_deg 10.036 r_scangle_it 6.281 r_scbond_it 4.344 r_mcangle_it 2.781 r_mcbond_it 1.582 r_angle_refined_deg 1.326 r_angle_other_deg 0.925 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7278 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing